Chinese softshell turtle vs Painted turtle LastZ results
Chinese softshell turtle (Pelodiscus sinensis, PelSin_1.0) and Painted turtle (Chrysemys picta bellii, Chrysemys_picta_bellii-3.0.3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 95. Chinese softshell turtle was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.
Configuration parameters
| Parameter | Value |
|---|---|
| Gap open penalty (O) | 400 |
| Gap extend penalty (E) | 30 |
| HSP threshold (K) | 3000 |
| Threshold for gapped extension (L) | 3000 |
| Threshold for alignments between gapped alignment blocks (H) | 2200 |
| Masking count (M) | |
| Seed and Transition value (T) | 1 |
| Scoring matrix (Q) | Default:
A C G T
91 -114 -31 -123
-114 100 -125 -31
-31 -125 100 -114
-123 -31 -114 91
|
Chunking parameters
| Parameter | Chinese softshell turtle | Painted turtle |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 1,921,965 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Chinese softshell turtle |
Uncovered: 1,017,018,413 out of 2,202,483,752 |
Uncovered: 1,663,410 out of 28,389,223 |
| Painted turtle |
Uncovered: 1,229,527,413 out of 2,365,766,571 |
Uncovered: 4,521,196 out of 33,484,189 |
Block size distribution
| Size range | All 1,921,965 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 41,146 |
265.1 kb |
|||
| 10 bp - 100 bp | 228,752 |
13.1 Mb |
42,994 |
3.0 Mb |
|
| 100 bp - 1 kb | 1,251,481 |
540.3 Mb |
151,467 |
55.0 Mb |
|
| 1 kb - 10 kb | 400,269 |
698.9 Mb |
31,258 |
67.7 Mb |
|
| 10 kb - 100 kb | 317 |
5.7 Mb |
2,264 |
69.5 Mb |
|
| 100 kb - 1 Mb | 1,335 |
496.1 Mb |
|||
| 1 Mb - 10 Mb | 303 |
567.0 Mb |
|||